Several attempts to resolve the phylogeny of turtles in the clade Geoemydidae using morphology have been unsuccessful, in part because of unusually high levels of polymorphism. This has hindered the integration of the geoemydid fossil record into a phylogenetic framework. Many methods, shown to improve phylogenetic inference, allow the incorporation of different amounts of state frequency information from polymorphic characters into a phylogenetic analysis. Here, we present a new character matrix for the shell of geoemydids and assess the performance of polymorphism coding methods ('majority', 'generalized frequency coding', 'polymorphic' and 'missing') in a phylogenetic analysis by comparing the result topology of each method with a reference molecular phylogeny. The four coding methods failed to recover trees that were both well resolved and highly congruent with the reference phylogeny. Moreover, contrary to previous studies, the coding methods that made more use of character states frequencies did not perform better. However, a leave-one-out subsampling analysis suggested that despite these problems, the new matrix can still be used to place fossils in the geoemydid phylogeny with some reliability. Finally, we provide a list of characters that diagnose the major clades in our molecular reference tree.

BackgroundTestudinoidea is a major clade of turtles that has colonized different ecological environments across the globe throughout the Tertiary. Aquatic testudinoids have a particularly rich fossil record in the Tertiary of the northern hemisphere, but little is known about the evolutionary history of the group, as the phylogenetic relationships of most fossils have not been established with confidence, in part due to high levels of homoplasy and polymorphism.MethodsWe here focus on describing a sample of 30 testudinoid shells, belonging to a single population that was collected from lake sediments from the middle to late Eocene (35–39 Ma) Na Duong Formation in Vietnam. The phylogenetic placement of this new material is investigated by integrating it and 11 other species of putative geoemydids from the Eocene and Oligocene to a recently published matrix of geoemydid turtles, that embraces the use of polymorphic characters, and then running a total-evidence analysis.ResultsThe new material is highly polymorphic, but can be inferred with confidence to be a new taxon, Banhxeochelys trani gen. et sp. nov. It shares morphological similarities with other southeastern Asian testudinoids, Isometremys lacuna and Guangdongemys pingi, but is placed phylogenetically at the base of Pan-Testuguria when fossils are included in the analysis, or as a stem geoemydid when other fossils are deactivated from the matrix. The vast majority of other putative fossil geoemydids are placed at the base of Pan-Testuguria as well.DiscussionThe phylogenetic placement of fossil testudinoids used in the analysis is discussed individually and each species compared to Banhxeochelys trani gen. et sp. nov. The high levels of polymorphism observed in the new taxon is discussed in terms of ontogenetic and random variability. This is the first time that a large sample of fossil testudinoids has its morphological variation described in detail.

The freshwater turtle Acanthochelys radiolata (Mikan, 1820) is endemic to the Atlantic Forest domain in Brazil and few studies have been done on the morphology, geographic variation and taxonomy of this species. In this paper we record the morphological variation, as well as sexual dimorphism and ontogenetic changes in A. radiolata throughout its distribution range. We analyzed 118 morphological characters from 41 specimens, both quantitative and qualitative, and performed statistical analyses to evaluate size and shape variation within our sample. Morphological analysis revealed that A. radiolata is a polymorphic species, especially regarding color and shape. Two color patterns were recognized for the carapace and three for the plastron. Diagnostic characteristics of the species, such as the rounded tubercles on the neck and the shallow dorsal sulcus between the 2^nd and 4^th vertebral scutes, varied considerably. Acanthochelys radiolata also showed a high level of ontogenetic variation characterized by a change on the color pattern of plastron and limbs starting from the 4^th month of life. Sexual size dimorphism was observed for the first time on nine morphometric variables and females showed larger sizes than males. Based on these results we conclude that A. radiolata represents one single polymorphic species distributed in the lowlands of the Brazilian Atlantic Forest from the state of Alagoas to the state of Rio de Janeiro and the south of Minas Gerais state.

Background. Studies on the geographic variation of the matamata, Chelus fimbriatus, have previously demonstrated differences between carapace shape, plastral pigmentation and the ventral coloration of the neck between populations from the Amazon and Orinoco river basins, but did not discuss whether these populations should be considered different species. The aim of this study is to evaluate the taxonomic status of C. fimbriatus and to describe its intraspecific and ontogenetic variability and sexual dimorphism based on morphology and osteology. Methods. We analyzed 277 morphological characters and 138 osteological characters of the skull and shell of 82 matamatas from the four known populations (Amazon, Orinoco, Guyana and Tocantins) and performed the Population Aggregation Analysis (PAA) species delimitation test in searching for character states that are exclusive to and fixed between populations. The t Student test was also performed in order to observe sexual dimorphism. Results. Considerable overlap in character states between different populations prevents the recognition of these populations as independent species. Chelus fimbriatus has a high level of polymorphism, particularly among morphological and color pattern characters. Unlike what have been stated on previous studies, we recognise four different carapace shapes, of which the anteriorly larger oval shape is the most common one. Two coloration patterns can be found both for the plastron and the carapace that are strongly correlated with one another, but no such correlation was observed with geographic distribution. We furthermore recognise three states of neck coloration pattern. Ontogenetic variability was observed in the coloration of the carapace, plastron, and the underside of the neck, in that juveniles have a stronger pigmentation than adults. Sexual dimorphism was established for six morphometric variables of the shell and 20 variables of the skull. As expected, females are significant larger than males for all these variables, such as carapace, plastron and skull length. New osteological characters, such as the presence of a serrated medial process in the palatine and a pair of anterolateral tubercles in the basioccipital were observed. Discussion. This is the first study to confirm the presence of sexual dimorphism in C. fimbriatus using morphological and morphometric variables and to document infraspecific variation in detail. The possible presence of two subspecies has been discussed since the 19th century based on alleged geographic variation in coloration patterns. However, this hypothesis could not be confirmed in the context of this study and the matamata should therefore still be considered a single species with a wide distribution range.